Ah, the eternal problem.
If you make your leaders larger to hold the flag bridge, they are obvious and easily targetted. If you remove a weapon or two to fit the flag bridge, they are slightly less obvious yet still easily targetted. Weaken the defenses (speed, shields, armour, or PD) and while they are hard to identify they are more easily destroyed.
Personally, I usually end up with a significantly improved leader class (rather than simple variant) that adds extra speed & defense as well as the flag bridge. Sometimes I go whole hog and use light cruiser leaders for destroyer squadrons and battlecruiser leaders for cruiser squadrons, etc.